Photographic film scanners are known in which image frames on a strip of photographic film are scanned to convert the optical image frames into digital image data which can be stored and manipulated in a computer and, at the user's option, sent to a digital printer for generating hardcopy image prints. It is common in such scanners, to scan the image frame by transporting the film strip through an optical imaging path in which an exposure light source is shone through the image and focussed onto a linear CCD sensor to capture the image information one scan line at a time. The exposure light source may comprise a linear, interleaved array of spectrally distinct light emitting diodes (LED), for example, emitting in the red, blue and green spectra. In order to achieve accurate color rendition in the scanner it is necessary to perform a calibration of the LED exposure lights primarily to equalize the light outputs of the respective red, blue and green LED's. The analog pixel-by-pixel image information captured on the linear CCD light sensor must be clocked out of the CCD, digitized, processed and transferred to a host computer in synchronism with the transport motion of the film in such a manner that the transferred data is accurate and that no data is lost as a result of asynchronous operation between the scanner and the host computer. Internal operations of the scanner typically involve the use of separate timers to control the light source, film transport motor drive and data clocking/transfer functions, which require complex synchronizing provisions for control of the separate timers. Changing the scanning resolution complicates the control procedure as does changing the operating conditions of the R, B, G exposure light sources to accommodate for system drift and differing density characteristics among different film strips. It is an objective of the present invention to provide a simple and effective control method and apparatus for operating a film scanner that simplifies the synchronizing of the various operating functions and also simplifies implementation of changes in operating conditions of the scanner.